freebsd-ports/biology/py-cutadapt/Makefile

PORTNAME=	cutadapt
DISTVERSION=	3.3
PORTREVISION=	1
CATEGORIES=	biology python
MASTER_SITES=	PYPI
PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}

MAINTAINER=	jwb@FreeBSD.org
COMMENT=	Trim adapters from high-throughput sequencing reads
WWW=		https://pypi.org/project/cutadapt/

LICENSE=	MIT
LICENSE_FILE=	${WRKSRC}/LICENSE

BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools_scm>0:devel/py-setuptools_scm@${PY_FLAVOR}
RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen==1.1:archivers/py-xopen@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}dnaio==0.5.1:biology/py-dnaio@${PY_FLAVOR}
TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}pytest-timeout>0:devel/py-pytest-timeout@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR}

USES=		python
USE_PYTHON=	autoplist concurrent cython distutils

post-install:
	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so

do-test:
	@cd ${WRKSRC} && ${PYTHON_CMD} -m pytest

.include <bsd.port.mk>
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00			`PORTNAME= cutadapt`
py-cutadapt: Update to 3.3 Numerous small bug fixes and enhancements, code refactoring py-xopen: Update to 1.1.0 Required by cutadapt 3.3 Drop python 3.5 support Add isal support (not yet utilized in FreeBSD port) 2021-03-06 18:55:38 +01:00			`DISTVERSION= 3.3`
biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 15:20:39 +02:00			`PORTREVISION= 1`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00			`CATEGORIES= biology python`
/: rename CHEESESHOP to PYPI in MASTER_SITES PR: 267994 Differential revision: D37518 Approved by: bapt 2023-01-11 16:47:15 +01:00			`MASTER_SITES= PYPI`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00			`PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}`

			`MAINTAINER= jwb@FreeBSD.org`
biology/py-cutadapt: Upgrade to 1.18 Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D17099 2018-09-20 16:10:52 +02:00			`COMMENT= Trim adapters from high-throughput sequencing reads`
Add WWW entries to port Makefiles It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner) 2022-09-07 23:06:12 +02:00			`WWW= https://pypi.org/project/cutadapt/`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00
			`LICENSE= MIT`
biology/py-cutadapt: Upgrade to 1.18 Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D17099 2018-09-20 16:10:52 +02:00			`LICENSE_FILE= ${WRKSRC}/LICENSE`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00
biology/py-cutadapt: Upgrade to 2.1 Add do-test target 2019-03-24 22:20:24 +01:00			`BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools_scm>0:devel/py-setuptools_scm@${PY_FLAVOR}`
Unbreak INDEX 2021-03-06 22:18:14 +01:00			`RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen==1.1:archivers/py-xopen@${PY_FLAVOR} \`
biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 15:20:39 +02:00			`${PYTHON_PKGNAMEPREFIX}dnaio==0.5.1:biology/py-dnaio@${PY_FLAVOR}`
biology/py-cutadapt: Upgrade to 2.1 Add do-test target 2019-03-24 22:20:24 +01:00			`TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \`
biology/py-cutadapt: fix tests by adding missing test depend Approved by: portmgr blanket 2022-04-07 01:20:09 +02:00			`${PYTHON_PKGNAMEPREFIX}pytest-timeout>0:devel/py-pytest-timeout@${PY_FLAVOR} \`
			`${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR}`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00
all: remove explicit versions in USES=python for "3.x+" The logic in USES=python will automatically convert this to 3.8+ by itself. Adjust two ports that only had Python 3.7 mentioned but build fine on Python 3.8 too. finance/quickfix: mark BROKEN with PYTHON libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option] QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found ^~~~~~~~~~ 1 warning and 1 error generated. Reviewed by: portmgr, vishwin, yuri Differential Revision: <https://reviews.freebsd.org/D40568> 2023-06-15 00:00:28 +02:00			`USES= python`
biology/py-cutadapt: Upgrade to 2.1 Add do-test target 2019-03-24 22:20:24 +01:00			`USE_PYTHON= autoplist concurrent cython distutils`
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00
			`post-install:`
			`@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so`

biology/py-cutadapt: Upgrade to 2.1 Add do-test target 2019-03-24 22:20:24 +01:00			`do-test:`
			`@cd ${WRKSRC} && ${PYTHON_CMD} -m pytest`

[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 2017-11-29 23:17:43 +01:00			`.include <bsd.port.mk>`